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17  structures 266  species 0  interactions 9123  sequences 109  architectures

Family: Cu_bind_like (PF02298)

Summary: Plastocyanin-like domain

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Plastocyanin-like domain Provide feedback

This family represents a domain found in flowering plants related to the copper binding protein plastocyanin. Some members of this family (eg P93328) may not bind copper due to the lack of key residues.

Literature references

  1. Greene EA, Erard M, Dedieu A, Barker DG; , Plant Mol Biol 1998;36:775-783.: MtENOD16 and 20 are members of a family of phytocyanin-related early nodulins. PUBMED:9526510 EPMC:9526510

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR003245

Among the blue copper proteins with a single type I (or "blue") mononuclear copper site, the plant-specific phytocyanins constitute a distinct subfamily that can be further subdivided into the families of uclacyanins, stellacyanins, plantacyanins, and early nodulins. Stellacyanins have a blue copper coordinated by two His, one Cys and one Gln. In plantacyanins and uclacyanins, the ligands of the type-I Cu sites are two His, one Cys and one Met [ PUBMED:9761472 , PUBMED:11085657 , PUBMED:15858169 , PUBMED:15631465 ]. Early nodulins lack amino acid residues that coordinate Cu, so they are believed to be involved in unknown processes without binding Cu [ PUBMED:19897921 ]. Phytocyanins are found in chloropasts of higher plants.

The phytocyanin domain has a core of seven polypeptide strands arranged as a beta-sandwich comprising two beta-sheets, beta-sheet I and beta-sheet II. Beta-sheet I consists of three beta-strands and beta-sheet II consists of four beta-strands. A disulfide bridge close the metal centre is characteristic for phytocyanins, in contrast to azurins, pseudoazurins, and plastocyanins, where a disulfide bond is located on the distal side of the beta-barrel. This disuldide bridge may play a crucial role in maintaining the tertiary structure of the protein and/or the formation of the copper binding centre because one of the His ligands of copper is followed directly by a bridging Cys residue [ PUBMED:9761472 , PUBMED:11085657 , PUBMED:15858169 , PUBMED:15631465 ]. Some members of this family (P93328) may not bind copper due to the lack of key residues.

Some proteins known to contain a phytocyanin domain are listed below:

  • Cucumber basic protein (CBP).
  • Spinach basic protein (SBP).
  • Cucumber stellacyanin (CST).
  • Zucchini mavicyanin.
  • Horseradish umecyanin [ PUBMED:5089608 , PUBMED:11945593 ].

Some of the proteins in this family are allergens. The allergens in this family include allergens with the following designations: Amb a 3.

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan CU_oxidase (CL0026), which has the following description:

Many of the proteins in this family contain multiple similar copies of this plastocyanin-like domain.

The clan contains the following 15 members:

Copper-bind COX2 COX_ARM Cu-oxidase Cu-oxidase_2 Cu-oxidase_3 Cu_bind_like Cupredoxin_1 CzcE DP-EP Ephrin hGDE_N PAD_N PixA SoxE


We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

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HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...


This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

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Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Pfam-B_398 (release 5.2)
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Mian N , Bateman A
Number in seed: 15
Number in full: 9123
Average length of the domain: 82.50 aa
Average identity of full alignment: 31 %
Average coverage of the sequence by the domain: 43.21 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.8 20.8
Trusted cut-off 20.8 20.8
Noise cut-off 20.7 20.7
Model length: 84
Family (HMM) version: 19
Download: download the raw HMM for this family

Species distribution

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For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Cu_bind_like domain has been found. There are 17 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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